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Table 6 Computing performance of major functions using 23 exome sequencing samples on a 16 CPU workstation

From: SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data

Script Function #CPU Peak RAM
(Gb)
Time Notes
exon_qc quality control 1 6 10-20 min Per sample
sam2wig generate wig file 1 2 20-50 min Per sample
sam2pileup generate pileup file 1 3-7 1-4 hours Per sample
snp annotate and filter snp and indels 1 4 2-8 min Per sample
rpkm quantify coverage on gene model 1 4 4-16 min Per sample
cnv copy number variation 1 4 5 min Per sample
genotyping genotyping file across samples 1 8 4 hour Across 23 samples
phenotyping coverage (expression) across samples 1 5 10 min Across 23 samples
eqtl -m cis Cis- EQTL 1 3 1 hour 1000 genome data
eqtl -m trans Trans-EQTL 16 * 3 7 days 1000 genome data